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Yorodumi- PDB-2v2e: Structure of isoniazid (INH) bound to cytochrome c peroxidase mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2e | ||||||
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Title | Structure of isoniazid (INH) bound to cytochrome c peroxidase mutant N184R Y36A | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / CYTOCHROME C PEROXIDASE / TRANSIT PEPTIDE / ORGANIC RADICAL / HYDROGEN PEROXIDE / INH / CCP / IRON / HEME / ISONIAZID / PEROXIDASE / MITOCHONDRION / METAL-BINDING | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Metcalfe, C.L. / Macdonald, I.K. / Brown, K.A. / Raven, E.L. / Moody, P.C.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: The Tuberculosis Prodrug Isoniazid Bound to Activating Peroxidases. Authors: Metcalfe, C.L. / Macdonald, I.K. / Murphy, E.J. / Brown, K.A. / Raven, E.L. / Moody, P.C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v2e.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2e.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2e ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2e | HTTPS FTP |
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-Related structure data
Related structure data | 2v23SC 2vcfC 2vcnC 2vcsC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33583.406 Da / Num. of mol.: 1 / Fragment: RESIDUES 71-361 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PT7CCP/Y39A/N184R / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-ISZ / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.84 % / Description: NONE |
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Crystal grow | Method: microdialysis / pH: 6 Details: MICRODIALYSIS INTO 50MM POTASSIUM PHOSPHATE, PH 6.0 CONTAINING 30% V/V MPD. ISONIAZID WAS DISSOLVED INTO THE MOTHER LIQUOR (300MM) AND SOAKED INTO THE CRYSTAL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: XENOCS MULTI-LAYER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→30.28 Å / Num. obs: 38990 / % possible obs: 81.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.8 / % possible all: 20.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V23 Resolution: 1.68→30.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.047 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→30.28 Å
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Refine LS restraints |
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